tests/testthat/testthat.R

In SeqGate: Filtering of Lowly Expressed Features

context("check applySeqGate function")
library(SeqGate)

## Generate test data

cond<-c("A","A","B","B","A","B")
nrow=100
ncol=6
counts <- rnbinom(n = (nrow*ncol), size = 2, mu=100)

counts_with_zeros<-matrix(counts,nrow=nrow)
for(i in seq(1,nrow,round(nrow/10))){
    counts_with_zeros[i,]<-c(0,0,100,150,i,80)
    counts_with_zeros[i,]<-c(50,60,(10+i),0,55,0)
}
counts_with_zeros[c(2,12),] <- rep(0,ncol)
rownames(counts_with_zeros) <- paste("gene",c(1:nrow),sep="")


counts_no_zeros <- matrix(c(rep(c(5,10,20),4)),nrow=3,ncol=ncol)

counts_dec <- matrix(c(rep(c(5.1,0,10.2,20.1,6.4,7.9,40.5),6)),nrow=7,ncol=ncol)
counts_dec[1,c(2,5)]<-c(0,0)
counts_dec[5,c(1,2)]<-c(0,0)
counts_dec[3,c(4,6)]<-c(0,0)
counts_dec[6,c(3,6)]<-c(0,0)

counts_few_zeros <- matrix(c(rep(c(5,0,10,20),6)),nrow=4,ncol=ncol)
counts_few_zeros[1,c(2,5)]<-c(0,0)
counts_few_zeros[3,c(4,6)]<-c(0,0)

badcond<-c("A","B","C","D","E","F")

rowData <- DataFrame(row.names=rownames(counts_with_zeros))
colData <- DataFrame(Conditions=cond, row.names=LETTERS[1:6])
counts_with_zeros_SE <- SummarizedExperiment(
                        assays=list(counts=counts_with_zeros),
                        rowData=rowData, colData=colData)

counts_dec_SE <- SummarizedExperiment(
                        assays=list(counts=counts_dec),
                        colData=colData)

counts_no_zeros_SE <- SummarizedExperiment(
                        assays=list(counts=counts_no_zeros),
                        colData=colData)
                        
counts_noO_in_rep <- matrix(c(rep(c(0,10,20),6)),nrow=3,ncol=6)
counts_noO_in_rep_SE <- SummarizedExperiment(
                        assays=list(counts=counts_noO_in_rep),
                        colData=colData)
Conditions<-NULL
counts_with_zeros_badCond_SE <- SummarizedExperiment(
                        assays=list(counts=counts_with_zeros),
                        rowData=rowData, 
                        colData=DataFrame(Conditions=badcond))
                        
counts_few_zeros_SE <- SummarizedExperiment(
                        assays=list(counts=counts_few_zeros),
                        colData=colData)


## Perfom tests

test_that("applySeqGate function gives appropriate results in normal usage", {
    expect_output(res <- applySeqGate(counts_with_zeros_SE,"counts","Conditions"),"The SeqGate filter parameters applied are")
    expect_output(resD <- applySeqGate(counts_dec_SE,"counts","Conditions"),"The SeqGate filter parameters applied are")
    expect_s4_class(res,"SummarizedExperiment")
    expect_type(metadata(res)$threshold,"double")
    expect_type(rowData(res)$onFilter,"logical")
    expect_output(applySeqGate(counts_with_zeros_SE,"counts","Conditions",0.5,0.4,0.6),"The SeqGate filter parameters applied are")
})

test_that("applySeqGate function gives appropriate results in extreme usage", {
    expect_error(applySeqGate(counts_no_zeros_SE,"counts","Conditions"),"Data does not contain zero counts")
    expect_error(applySeqGate(counts_noO_in_rep_SE,"counts","Conditions"),"Impossible to calculate the distribution of max counts.")
})

test_that("applySeqGate function returns warning in extreme or weird situations", {
    expect_warning(applySeqGate(counts_with_zeros_SE,"counts","Conditions",percentile=0),"percentile == 0")
    expect_output(applySeqGate(counts_with_zeros_SE,"counts","Conditions",percentile=1),"The SeqGate filter parameters applied are")
    expect_output(applySeqGate(counts_with_zeros_SE,"counts","Conditions",propUpThresh=1),"The SeqGate filter parameters applied are")
})

test_that("applySeqGate returns the good error messages", {
    expect_error(applySeqGate(counts_with_zeros_SE,counts,"Conditions"),"assayName must be of character type")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts",Conditions),"colCond must be of character type")
    data2 <- cbind.data.frame(rownames(counts_with_zeros),counts_with_zeros)
    data2_SE <- SummarizedExperiment(assays=list(counts=data2))
    expect_error(applySeqGate(data2_SE,"counts","Conditions"),"contains non numeric columns")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts","Conditions",prop0=50),"prop0 must be >0 and <1")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts","Conditions",prop0=0),"prop0 must be >0 and <1")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts","Conditions",prop0=1),"prop0 must be >0 and <1")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts","Conditions",percentile=95),"percentile must be comprised between 0 and 1.")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts","Conditions",propUpThresh=0),"propUpThresh must be >0 and <=1.")
    expect_error(applySeqGate(counts_with_zeros_SE,"counts","Conditions",propUpThresh=-5),"propUpThresh must be >0 and <=1.")
    expect_error(applySeqGate(counts_with_zeros_badCond_SE,"counts","Conditions"),"Condition vector does not contain replicates.")
    expect_error(applySeqGate(counts_few_zeros_SE,"counts","Conditions"),"Too few zeros along with counts in condition")
})